Enhanced loss of retinoic acid network genes in Xenopus laevis achieves a tighter signal regulation

Retinoic acid (RA) is a major regulatory signal during embryogenesis produced from vitamin A (retinol) by an extensive, autoregulating metabolic and signaling network to prevent fluctuations that result in developmental malformations. Xenopus laevis is an allotetraploid hybrid frog species whose genome includes L (long) and S (short) chromosomes from the originating species. Evolutionarily, the X. laevis subgenomes have been losing either L or S homoeologs in about 43% of genes to generate singletons. In the RA network, out of the 47 genes, about 46% have lost one of the homoeologs, like the genome average. In contrast, RA metabolism genes from storage (retinyl esters) to retinaldehyde production exhibit enhanced gene loss with 75% singletons out of 28 genes. The effect of this gene loss on RA signaling autoregulation was studied. Employing transient RA manipulations, homoeolog gene pairs were identified in which one homeolog exhibits enhanced responses or looser regulation than the other, while in other pairs both homoeologs exhibit similar RA responses. CRISPR/Cas9 targeting of individual homoeologs to reduce their activity supports the hypothesis where the RA metabolic network gene loss results in tighter network regulation and more efficient RA robustness responses to overcome complex regulation conditions.

Interaction between Signal Pathways upon Formation of Plant Defense in Response to Environmental Stress Factors

In the course of evolution, plants have developed numerous specific regulatory signal pathways, which are hormonal for the most part. Phytohormones comprise not only such generally recognized endogenous growth regulators as abscisic acid, auxins, cytokinins, gibberellins, brassinosteroids (BS), ethylene, salicylic acid (SA), and jasmonates but also recently described derivatives of apocarotenoids—strigolactones (SL). Signal pathways interact at the level of biosynthesis of messengers and their translocation as well as upon activation of target genes. Since abiotic and biotic environmental stressors negatively influence plant productivity, understanding of molecular mechanisms of regulation induced by stress agents may help researchers to produce stress-resistant and high-yielding plants using molecular techniques. This paper is a review of present-day literature dealing with the interaction and interference of nonhormonal and hormonal signals regulating growth and development of plants under ever-changing environmental conditions.

Self-association of MreC as a regulatory signal in bacterial cell wall elongation

The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the cytoskeletal element MreB and regulates the activity of cell wall biosynthesis enzymes, in a process that may be dependent on MreC self-association. Here, we use electron cryo-microscopy and X-ray crystallography to determine the structure of a self-associated form of MreC from Pseudomonas aeruginosa in atomic detail. MreC monomers interact in head-to-tail fashion. Longitudinal and lateral interfaces are essential for oligomerization in vitro, and a phylogenetic analysis of proteobacterial MreC sequences indicates the prevalence of the identified interfaces. Our results are consistent with a model where MreC’s ability to alternate between self-association and interaction with the cell wall biosynthesis machinery plays a key role in the regulation of elongasome activity.

S-Like Ribonuclease T2 Genes Are Induced during Mobilisation of Nutrients in Cotyledons from Common Bean

Germination and seedling development are crucial phases in a plant’s life cycle with economical and agronomical implications. The RNA quality in seeds is linked to seed viability, being an important agronomic trait since this leads to a loss in germination efficiency. In addition, RNA can be an important phosphorous reservoir in seeds, affecting the efficiency of the mobilisation of nutrients towards the seedlings. However, knowledge about the physiological function of ribonucleases during germination and seedling development is scarce. We analysed the ribonuclease activities of cotyledons during these processes and the expression of S-like ribonucleases T2. Ribonuclease activity was detected in cotyledons at 1 day after imbibition and the specific activity increased during germination and seedling development, reaching a maximal value at 10 days after imbibition. At this stage, the levels of proteins and RNA in cotyledons were very low. Using in-gel assays, three ribonucleases were detected with apparent molecular masses of 16, 17 and 19 kDa along cotyledon ontogeny. The S-like ribonucleases T2 family consists of four genes in common bean (PvRNS1 to PvRNS4). The expression of PvRNS1, PvRNS2 and PvRNS4 increased in the phase of nutrient mobilisation in cotyledons. The expression of PvRNS1 increased 1000 fold in cotyledons, from 1 to 6 days after imbibition. The suppression of the induction of ribonuclease activity and gene expression in decapitated seedlings suggests that the regulatory signal comes from the developing axes. These results clearly state that S-like ribonucleases T2 are involved in RNA turnover in cotyledons during seedling development.

Chromatin topology and the timing of enhancer function at theHoxDlocus

TheHoxDgene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different subgroups ofHoxdgenes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate from two distinct topologically associating domains (TADs) flankingHoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory submodules. To understand the importance of this particular regulatory topology to controlHoxdgene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites, or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation ofHoxdgenes illustrate the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts was eventually resumed, showing that the presence of enhancer sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavorable orientation of CTCF sites.

Limit cycles in models of circular gene networks regulated by negative feedback loops

Background The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal reception and its implementation, provide natural conditions for complicated dynamic regimes in these systems. The delay phenomenon at the intracellular level is a consequence of the matrix principle of data transmission, implemented through the rather complex processes of transcription and translation.However, the rules of the influence of system structure on system dynamics are not clearly understood. Knowledge of these rules is particularly important for construction of synthetic gene networks with predetermined properties. Results We study dynamical properties of models of simplest circular gene networks regulated by negative feedback mechanisms. We have shown existence and stability of oscillating trajectories (cycles) in these models. Two algorithms of construction and localization of these cycles have been proposed. For one of these models, we have solved an inverse problem of parameters identification. Conclusions The modeling results demonstrate that non-stationary dynamics in the models of circular gene networks with negative feedback loops is achieved by a high degree of non-linearity of the mechanism of the autorepressor influence on its own expression, by the presence of regulatory signal delay, the value of which must exceed a certain critical value, and transcription/translation should be initiated from a sufficiently strong promoter/Shine-Dalgarno site. We believe that the identified patterns are key elements of the oscillating construction design.